So I installed Fedora 18 on a couple of machines, and I lost total control of my audio volumes. What tipped me off, was my internal audio speaker playing the same thing that my earphones were. I decided to delve in, and realised that I needed to install alsamixer (a console curses based application) to mute my internal (called "Mono") speaker. The alsamixer had more sliders and knobs than well, anything. It had every component of my audio card.

When I went into some of the other machines, I also realised that instead of granular control of each device, I was given one slider for everything and no granular control. (i.e.: headphone, mic boost, PCM, IEC958, Beep, Internal Mic Boost, etc.) All of these options were replaced by a couple of sliders ambiguously named.

After some more digging, I realised that it was a result of pulseaudio. Instead of phonon to use pulseaudio you needed to tell it to use alsa. Instead of removing the entire pulseaudio stack, which would break many things, a simple "sudo yum remove pulseaudio-2.1-5.fc18" regained all of my fine tuned controls.